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Abstract Background The aim of this study was to evaluate the condylar morphological changes after orthodontic treatment in adult patients with Class II malocclusion using a Cone-beam computed tomography (CBCT). Methods Images of twenty-eight adult patients with Class II malocclusion who have no temporomandibular symptoms were involved in this study. To analyze the post-treatment changes in condylar morphology, mimics 17.0 software was used to measure several values and reconstruct the three-dimensional condyle, including height of the condyle, area and bone mineral density of the maximum axial and sagittal section, volume and bone mineral density of the three-dimensional condyle and condylar head before and after orthodontic treatment. Using SPSS 19.0 software package Paired t-test was applied for comparison of condylar morphology analysis between pre-treatment and post-treatment. Results Height of condylar head increase significant (P < .05). Bone mineral density showed a decrease in the maximum axial and sagittal section, three-dimensional condyle and condylar head (P < .01). Evaluation of volume revealed that volume of both condyle and condylar head decrease considerably (P < .05). No significant difference was detected in other values ((P > .05). Conclusion Condylar volume decreased and height of condylar head have changed, so we speculated that adaptive bone remodeling of the condyle occurs.